ukbiobank-omop-etl

Resources and documentation for UK Biobank to OMOP CDM v5.3.1 conversion

View the Project on GitHub thehyve/ukbiobank-omop-etl

Table name: condition_occurrence

Reading from Cancer register

Cancer EHR Acquired from national registries.

Destination Field Source field Logic Comment field
condition_occurrence_id      
person_id      
condition_start_date 40005-16.0    
condition_concept_id 40006-16.0
40011-16.0
Combine with 40011 (histology) to map to a SNOMED cancer condition. - see also convention of the OHDSI oncology wg
 
condition_start_datetime      
condition_end_date      
condition_end_datetime      
condition_type_concept_id      
stop_reason      
provider_id      
visit_occurrence_id      
visit_detail_id      
condition_source_value 40006-16.0    
condition_source_concept_id 40006-16.0    
condition_status_source_value      
condition_status_concept_id      

Reading from Medical conditions

Destination Field Source field Logic Comment field
condition_occurrence_id      
person_id      
condition_start_date      
condition_concept_id      
condition_start_datetime      
condition_end_date      
condition_end_datetime      
condition_type_concept_id      
stop_reason      
provider_id      
visit_occurrence_id      
visit_detail_id      
condition_source_value      
condition_source_concept_id      
condition_status_source_value      
condition_status_concept_id